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From phenotype to genotype: an association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs
- Source :
- Bioinformatics
- Publication Year :
- 2012
-
Abstract
- Motivation: Imaging genetic studies typically focus on identifying single-nucleotide polymorphism (SNP) markers associated with imaging phenotypes. Few studies perform regression of SNP values on phenotypic measures for examining how the SNP values change when phenotypic measures are varied. This alternative approach may have a potential to help us discover important imaging genetic associations from a different perspective. In addition, the imaging markers are often measured over time, and this longitudinal profile may provide increased power for differentiating genotype groups. How to identify the longitudinal phenotypic markers associated to disease sensitive SNPs is an important and challenging research topic. Results: Taking into account the temporal structure of the longitudinal imaging data and the interrelatedness among the SNPs, we propose a novel ‘task-correlated longitudinal sparse regression’ model to study the association between the phenotypic imaging markers and the genotypes encoded by SNPs. In our new association model, we extend the widely used ℓ2,1-norm for matrices to tensors to jointly select imaging markers that have common effects across all the regression tasks and time points, and meanwhile impose the trace-norm regularization onto the unfolded coefficient tensor to achieve low rank such that the interrelationship among SNPs can be addressed. The effectiveness of our method is demonstrated by both clearly improved prediction performance in empirical evaluations and a compact set of selected imaging predictors relevant to disease sensitive SNPs. Availability: Software is publicly available at: http://ranger.uta.edu/%7eheng/Longitudinal/ Contact: heng@uta.edu or shenli@inpui.edu
- Subjects :
- Statistics and Probability
Genotype
Single-nucleotide polymorphism
Computational biology
Disease
Biology
Biochemistry
Polymorphism, Single Nucleotide
03 medical and health sciences
0302 clinical medicine
Polymorphism (computer science)
Alzheimer Disease
SNP
Humans
Molecular Biology
Genetic Association Studies
030304 developmental biology
Genetics
0303 health sciences
Bioinformatics of Health and Disease, Biomarkers and Personalized Medicine
Regression analysis
Phenotype
Original Papers
Regression
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
Regression Analysis
030217 neurology & neurosurgery
Algorithms
Subjects
Details
- ISSN :
- 13674811
- Volume :
- 28
- Issue :
- 18
- Database :
- OpenAIRE
- Journal :
- Bioinformatics (Oxford, England)
- Accession number :
- edsair.doi.dedup.....942d413ad02e96770f7d9df9184537d9